Package: spammR 0.99.26

Sara Gosline

spammR: SPatial Analysis of Multiomics Measurements in R

SpammR provides a suite of tools and a data structure to analyze diverse multiomics measurements in a spatial context. It enables the analysis and visualization of omics measurements paired with a specific image, each with spatial coordinates.

Authors:Sara Gosline [cre, aut], Harkirat Sohi [aut], Yannick Mahlich [aut]

spammR_0.99.26.tar.gz
spammR_0.99.26.zip(r-4.7-any)spammR_0.99.26.zip(r-4.6-any)spammR_0.99.26.zip(r-4.5-any)
spammR_0.99.26.tgz(r-4.6-any)spammR_0.99.26.tgz(r-4.5-any)
spammR_0.99.26.tar.gz(r-4.7-any)spammR_0.99.26.tar.gz(r-4.6-any)
spammR_0.99.26.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
spammR/json (API)

# Install 'spammR' in R:

install.packages('spammR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/pnnl-compbio/spammr/issues

Pkgdown/docs site:https://pnnl-compbio.github.io

Datasets:

oneKSoilsCoords - Soil sample coordinates for the sample information
oneKSoilsMeta - Soil samples from the 1000 soils project Row names indiciate KEGG Orthologs, Column names indicate locations Soil samples metadata for the sample information
pancMeta - Here is the data to be included in the spammR package
protMeta - Protein metadata for general uniprot data, including the pancProts column for the panc data
smallPancData - Pancreatic proteomics measurements from Gosline et al. proteomics study. Row names indicate individual proteins, columns indicate sample identifiers described in 'pancMeta'. Individual values show un-transformed abundance values for each protein. List of proteomic measurements in a list sorted from individual regions of the pancreas. A subset of the data at https://figshare.com/articles/dataset/spammR_Files/29250962

On BioConductor:spammR-0.99.26(bioc 3.24)

spatial pathways proteomics differentialexpression metabolomics systemsbiology geneexpression genesetenrichment software transcription sequencing microarray epigenetics cheminformatics transcriptomics coverage normalization preprocessing bayesian clustering regression exonarray rnaseq onechannel twochannel micrornaarray mrnamicroarray proprietaryplatforms singlecell cellbiology biomedicalinformatics functionalgenomics immunooncology alternativesplicing differentialsplicing batcheffect multiplecomparison qualitycontrol timecourse dataimport lipidomics

5.31 score 9 stars 10 scripts 194 downloads 13 exports 211 dependencies

Last updated from:6a00912bf8. Checks:1 NOTE, 7 WARNING, 1 ERROR, 1 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	207
linux-devel	WARNING	386
source / vignettes	ERROR	327
linux-release	WARNING	454
macos-release	WARNING	246
macos-oldrel	WARNING	248
windows-devel	WARNING	232
windows-release	WARNING	255
windows-oldrel	WARNING	311
wasm-release	OK	168

Exports:calc_missingness calc_spatial_diff_ex convert_to_spe distance_based_analysis enrich_gradient enrich_ora impute_spe retrieve_metaspace_data spat_reduce spatial_heatmap spatial_network split_spe volcano_plot

Dependencies:abind askpass backports base64enc Biobase BiocFileCache BiocGenerics BiocManager BiocStyle bit bit64 bitops blob bookdown boot broom bslib cachem callr car carData caTools cellranger class classInt cli clipr colorspace conflicted corrplot cowplot cpp11 crayon crosstalk curl data.table DBI dbplyr DelayedArray deldir Deriv digest doBy dplyr DT dtplyr e1071 evaluate farver fastmap filelock fontawesome forcats forecast Formula fracdiff fs gargle generics GenomicRanges ggforce ggnewscale ggplot2 ggpubr ggraph ggrepel ggsci ggsignif glue googledrive googlesheets4 gplots graphlayouts gridExtra gtable gtools haven here highr hms htmltools htmlwidgets httr httr2 ids igraph impute IRanges isoband jquerylib jsonlite KernSmooth knitr labeling later lattice lazyeval leapR lifecycle limma lme4 lmtest lubridate magick magrittr MASS Matrix MatrixGenerics MatrixModels matrixStats memoise mgcv mime minqa modelr nlme nloptr nnet numDeriv openssl otel pbkrtest pillar pkgconfig plotly png polyclip polynom prettyunits processx progress promises proxy ps purrr quantreg R6 ragg rappdirs rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen RcppTOML Rdpack readr readxl reformulas rematch rematch2 reprex reticulate rjson rlang rmarkdown rprojroot RSQLite rstatix rstudioapi rvest s2 S4Arrays S4Vectors S7 sass scales selectr Seqinfo sf SingleCellExperiment sp SparseArray SparseM SpatialExperiment spData spdep statmod stringi stringr SummarizedExperiment survival sys systemfonts terra textshaping tibble tidygraph tidyr tidyselect tidyverse timechange timeDate tinytex tweenr tzdb units urca utf8 uuid vctrs viridis viridisLite vroom withr wk xfun xml2 XVector yaml zoo

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Calculate centers of spots/samples for distance based analysis	calc_centers
Helper function for computing pairwise differences between sample values	calc_diff_pairwiseSamples
Calculate degree of missingness for each featurea and sample	calc_missingness
Identify differentially abundant features across image	calc_spatial_diff_ex
Create a 'SpatialExperiment' object from data	convert_to_spe
Identify multiomic features correlated with an distance to an image feature	distance_based_analysis
Calculate functional or pathway enrichment from a gradient	enrich_gradient
Calculate functional or pathway enrichment	enrich_ora
Impute missing values based on spatial coordinates	impute_spe
Soil sample coordinates for the sample information	oneKSoilsCoords
Soil samples from the 1000 soils project Row names indiciate KEGG Orthologs, Column names indicate locations Soil samples metadata for the sample information	oneKSoilsMeta
Here is the data to be included in the spammR package	pancMeta
Protein metadata for general uniprot data, including the pancProts column for the panc data	protMeta
Retrieve data objects from metaspace	retrieve_metaspace_data
Pancreatic proteomics measurements from Gosline et al. proteomics study. Row names indicate individual proteins, columns indicate sample identifiers described in 'pancMeta'. Individual values show un-transformed abundance values for each protein. List of proteomic measurements in a list sorted from individual regions of the pancreas. A subset of the data at https://figshare.com/articles/dataset/spammR_Files/29250962	smallPancData
Reduce a high resolution image measurement (origin) to a lower resolution measurement (target)	spat_reduce
Plot data in heatmap together with image	spatial_heatmap
Plot network of correlated features	spatial_network
Divide SPE object into smaller objects by column features	split_spe
Create a volcano plot from differential expression data	volcano_plot